Summary of study ST001232

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000825. The data can be accessed directly via it's Project DOI: 10.21228/M81X1W This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST001232
Study TitleCombining stage - specificity and metabolomic profiling to advance drug discovery for malaria
Study TypeDrug Exposure
Study SummaryMetabolic examination/confirmation of MoA stage-specificity observed in study
Institute
Pennsylvania State University
DepartmentBMB
LaboratoryLlinás Laboratory
Last NameOwen
First NameEdward
Address6014 Goldenrod Court
Emaileso5005@psu.edu
Phone8144045235
Submit Date2019-07-09
Analysis Type DetailLC-MS
Release Date2020-03-03
Release Version1
Edward Owen Edward Owen
https://dx.doi.org/10.21228/M81X1W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000825
Project DOI:doi: 10.21228/M81X1W
Project Title:Combining stage - specificity and metabolomic profiling to advance drug discovery for malaria
Project Type:LC-MS Metabolomics
Project Summary:Hydrophilic LC-MS analysis of compounds as part of functional examination of metabolic impact in relation to stage-specificity of antimalarials
Institute:Pennsylvania State University
Department:BMB
Laboratory:Llinás Laboratory
Last Name:Llinás
First Name:Manuel
Address:W-122 Millennium Science Complex, Pollock Road
Email:eso5005@psu.edu
Phone:8148673527
Funding Source:This work was supported by the Bill and Melinda Gates Foundation ( OPP1054480 ) , the Medicines for Malaria Venture ( 08/0015 ) and the National Institutes of Health (R37 AI50234, R01 AI109023, R01 AI124678; R33 AI127581)

Subject:

Subject ID:SU001300
Subject Type:Cultured cells
Subject Species:Plasmodium Falciparum
Taxonomy ID:5833
Genotype Strain:3D7
Cell Strain Details:MR4-3D7
Subject Comments:All were MACS seperated Trophozoite infected red blood cells
Cell Counts:1x10^8 per technical replicate

Factors:

Subject type: Cultured cells; Subject species: Plasmodium Falciparum (Factor headings shown in green)

mb_sample_id local_sample_id Drug treatment
SA087885ATQ-04072018ATQ-04072018
SA087886ATQ-05102017ATQ-05102017
SA087887ATQ-06022018ATQ-06022018
SA087888ATQ-11022019ATQ-11022019
SA087889ATQ-11102018ATQ-11102018
SA087890ATQ-16032017ATQ-16032017
SA087891ATQ-18012018ATQ-18012018
SA087892ATQ-18102017ATQ-18102017
SA087893ATQ-21062017ATQ-21062017
SA087894ATQ-22092017ATQ-22092017
SA087895ATQ-26072017ATQ-26072017
SA087896ATQ-27062018ATQ-27062018
SA087897ATQ-29062017ATQ-29062017
SA087898DHA-30012018DHA-30012018
SA087899Ferroquine-06022018Ferroquine-06022018
SA087900GNF-Pf-5660-27062018GNF-Pf-5660-27062018
SA087901KAI407-29062017KAI407-29062017
SA087902Lumefantrine-30012018Lumefantrine-30012018
SA087923Mefloquine-30012018Mefloquine-30012018
SA087924MethyleneBlue-18012018MethyleneBlue-18012018
SA087903MMV000442-18102017MMV000442-18102017
SA087904MMV000787-22092017MMV000787-22092017
SA087905MMV007181-05102017MMV007181-05102017
SA087906MMV007181-22092017MMV007181-22092017
SA087907MMV019555-04072018MMV019555-04072018
SA087908MMV019555-26072017MMV019555-26072017
SA087909MMV020746-21062017MMV020746-21062017
SA087910MMV020746-22092017MMV020746-22092017
SA087911MMV021735-11102018MMV021735-11102018
SA087912MMV022224-11102018MMV022224-11102018
SA087913MMV022478-11022019MMV022478-11022019
SA087914MMV027496-11102018MMV027496-11102018
SA087915MMV030666-11102018MMV030666-11102018
SA087916MMV085071-04072018MMV085071-04072018
SA087917MMV665794-16032017MMV665794-16032017
SA087918MMV665939-21062017MMV665939-21062017
SA087919MMV667491-22092017MMV667491-22092017
SA087920MMV668311-11022019MMV668311-11022019
SA087921MMV675939-21062017MMV675939-21062017
SA087922MMV675939-22092017MMV675939-22092017
SA087925Naphthoquine-30012018Naphthoquine-30012018
SA087926Blank-18102017No treatment
SA087927Blank-30012018No treatment
SA087928Blank-16032017No treatment
SA087929Blank-11102018No treatment
SA087930Blank-29062017No treatment
SA087931Blank-04072018No treatment
SA087932Blank-06022018No treatment
SA087933Blank-18012018No treatment
SA087934Blank-26072017No treatment
SA087935Blank-05102017No treatment
SA087936Blank-22092017No treatment
SA087937Blank-27062018No treatment
SA087938Blank-21062017No treatment
SA087939Blank-11022019No treatment
SA087940Pipquine-18012018Pipquine-18012018
SA087941ND-26072017Treated with no drug
SA087942ND-22092017Treated with no drug
SA087943ND-27062018Treated with no drug
SA087944ND-30012018Treated with no drug
SA087945ND-21062017Treated with no drug
SA087946ND-29062017Treated with no drug
SA087947ND-05102017Treated with no drug
SA087948ND-06022018Treated with no drug
SA087949ND-04072018Treated with no drug
SA087950ND-11022019Treated with no drug
SA087951ND-11102018Treated with no drug
SA087952ND-18012018Treated with no drug
SA087953ND-16032017Treated with no drug
SA087954ND-18102017Treated with no drug
SA087955WLL-11022019WLL-11022019
Showing results 1 to 71 of 71

Collection:

Collection ID:CO001294
Collection Summary:Aspiration of 4 mL media, transfer of sample (1 mL) to 1.5 mL tubes
Sample Type:Cultured cells
Collection Method:Aspiration of 4 mL media, transfer of sample (1 mL) to 1.5 mL tubes
Collection Location:Biological safety hood
Collection Frequency:once after 2.5 hours treatment
Collection Duration:Collection and extraction occurs in under 20 minutes per plate
Volumeoramount Collected:1 mL containing 1x10^8 infected cells
Storage Conditions:On ice
Collection Vials:1.5 mL eppendorf
Storage Vials:1.5 mL eppendorf
Tissue Cell Quantity Taken:1 mL containing 1x10^8 infected cells

Treatment:

Treatment ID:TR001315
Treatment Summary:Infected Red Blood cells were exposed to Antimalarial Compounds, associated with sample names. No treatment (as in the case of blanks) denotes these samples did not undergo the treatment incubation (blanks are made at the point of extraction in this case), whereas treated with no drug relates that these samples (no drug or ND) underwent the same treatment incubation as other treated samples, but in this case as a negative control with no drug administered.
Treatment:Abiotic
Treatment Compound:Atovaquone, Dihydroartemisinin (DHA), Ferroquin (FQ), GNF-Pf-5660, KAI407, Lumefantrine (LMF), Methylene Blue, MMV00017 (Naphthoquine), MMV000442, MMV00787, MMV007181, MMV019555, MMV020746, MMV021735, MMV022224, MMV022478, MMV027496, MMV030666, MMV085071, MMV665794, MMV665939, MMV667491, MMV668311, MMV675939, Mefloquine (MQ), Piperaquine (PPQ), WLL
Treatment Route:Addition to media
Treatment Dose:10xIC50
Treatment Dosevolume:Always less than 10 uL per 5 mL sample
Treatment Doseduration:2.5 hours
Treatment Vehicle:Stocks kept in either DMSO or Water
Cell Storage:Temperature/Gas Mixture controlled incubator
Cell Growth Container:6-well plate
Cell Growth Config:5 mL per well, each with 1x10^8 cells
Cell Media:RPMI 1640 w/ Albumax, Gentamycin, Hypoxanthine, HEPES, Sodium Bicarbonate
Cell Harvesting:PBS Wash followed by 90% methanol extraction

Sample Preparation:

Sampleprep ID:SP001308
Sampleprep Summary:Samples washed in PBS, spun down, aspirated, extracted in 90% methanol with labelled aspartate, then dried, resuspended in water labelled with chlorpropamide
Sampleprep Protocol Filename:Metabolite_Extraction_for_LCMS_2017_Llinas.pdf
Processing Method:Wash, Lysis, Drying, resuspension
Processing Storage Conditions:On ice
Extraction Method:90% Methanol Lysis
Extract Cleanup:Centrifugation, pellet removal
Extract Storage:-80℃
Sample Resuspension:100 uL water with chlorpropamide
Sample Spiking:Labelled Aspartate, Chlorpropamide

Combined analysis:

Analysis ID AN002050
Analysis type MS
Chromatography type Normal phase
Chromatography system Thermo Dionex Ultimate 3000
Column XSelect T3 XP Column Reversed-Phase 2.5 µm Spherical Silica (2.1 mm x 100 mm)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap
Ion Mode NEGATIVE
Units peak area

Chromatography:

Chromatography ID:CH001489
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:XSelect T3 XP Column Reversed-Phase 2.5 µm Spherical Silica (2.1 mm x 100 mm)
Chromatography Type:Normal phase

MS:

MS ID:MS001902
Analysis ID:AN002050
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Blank subtraction, RSD cutoffs both by RSD per sample and pooled QCs to eliminate metabolites affected by time-dependency
Ion Mode:NEGATIVE
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